User: Johannes Rainer

gravatar for Johannes Rainer
Reputation:
840
Status:
Trusted
Location:
Italy
Twitter:
@jotsetung
Last seen:
2 days ago
Joined:
2 years, 7 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Center for Biomedicine, EURAC Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 185 results • page 1 of 19 • next >
0
votes
3
answers
68
views
3
answers
Answer: A: Is it possible to get Ensembl gene descriptions with ensembldb?
... OK, it's now available for Ensembl 87 (still working on the Ensembl 88) that you can get from AnnotationHub: > library(AnnotationHub) > ah <- AnnotationHub() > edb <- query(ah, "EnsDb.Hsapiens.v87") > edb EnsDb for Ensembl: |Backend: SQLite |Db type: EnsDb |Type of Gene ID: Ensem ...
written 11 days ago by Johannes Rainer840
0
votes
2
answers
69
views
2
answers
Comment: C: ensembldb salmon deseq2 txt2import right tool?
... I create EnsDbs for all species defined in Ensembl, this includes also Danio rerio. Once I'm done, these EnsDbs will show up in the AnnotationHub of the Bioc devel version. Note that the Danio rerio EnsDbs for Ensembl 87 and 88 are already in AnnotationHub ...
written 17 days ago by Johannes Rainer840
0
votes
1
answers
70
views
1
answers
Comment: C: BiocParallel: messages shown only when processes finished
... Thanks Martin for this explanation! ...
written 17 days ago by Johannes Rainer840
5
votes
1
answer
70
views
1
answer
BiocParallel: messages shown only when processes finished
... Hi, I am not quite sure if this is intentional, but I realized that calls to message and cat within functions executed by bplapply are shown only after the bplapply call. I tried to use also flush.console() after each message call but that didn't work either. library(BiocParallel) myFun <- fu ...
biocparallel written 17 days ago by Johannes Rainer840 • updated 17 days ago by Martin Morgan ♦♦ 20k
0
votes
2
answers
69
views
2
answers
Comment: C: ensembldb salmon deseq2 txt2import right tool?
... I am currently generating the EnsDbs for Ensembl 89 - it might take some days but then they should be available in Bioc devel's AnnotationHub.   ...
written 18 days ago by Johannes Rainer840
0
votes
2
answers
69
views
2
answers
Answer: A: ensembldb salmon deseq2 txt2import right tool?
... Hi Aaron, the warning message just means that the EnsDb.Rnorvegicus.v89 package is not available - as packages for the rat genome there are only EnsDb.Rnorvegicus.v75 and EnsDb.Rnorvegicus.v79 available that you could install using the biocLite function. If you need more recent gene models, you ca ...
written 18 days ago by Johannes Rainer840
0
votes
0
answers
71
views
0
answers
Comment: C: BiocParallel::bplapply() performance with MulticoreParam() is worse than mclappl
... Doesn't really answer your question, but since I also experienced problems with MulticoreParam on macOS... On mac i switched from MulticoreParam to DoparParam, i.e. I'm using the doParallel package for parallel processing. I had the feeling that multicore/MulticoreParam had a problem with the forks ...
written 18 days ago by Johannes Rainer840
0
votes
3
answers
152
views
3
answers
Comment: C: biomaRt - Error in getBM: The query to the BioMart webservice returned an invali
... Strange. It works also for me (see sessionInfo below); are you behind a proxy? R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin16.7.0/x86_64 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ ...
written 18 days ago by Johannes Rainer840
0
votes
3
answers
152
views
3
answers
Comment: C: biomaRt - Error in getBM: The query to the BioMart webservice returned an invali
... Regarding installation of AnnotationHub: you have to install it using biocLite: source("https://bioconductor.org/biocLite.R") biocLite("AnnotationHub")   Regarding biomaRt: you can still use biomaRt, I just wanted to provide an alternative solution. From time to time there might be problems with ...
written 21 days ago by Johannes Rainer840
0
votes
3
answers
152
views
3
answers
Answer: A: biomaRt - Error in getBM: The query to the BioMart webservice returned an invali
... Elaborating a little on Haiying's suggestion: first load one of the EnsDbs from AnnotationHub. They have an updated database scheme that provides a better mapping between Ensembl gene IDs and Entrezgene IDs (for Ensembl gene IDs mapping to multiple Entrezgene IDs you'll get all of them individually, ...
written 24 days ago by Johannes Rainer840

Latest awards to Johannes Rainer

Scholar 25 days ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 26 days ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 5 weeks ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 11 weeks ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 11 weeks ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 14 months ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
Scholar 14 months ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 14 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Popular Question 17 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Appreciated 18 months ago, created a post with more than 5 votes. For A: biomaRt no longer works with proxy after upgrade
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Centurion 19 months ago, created 100 posts.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 19 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 19 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Supporter 19 months ago, voted at least 25 times.
Scholar 20 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Autobiographer 2.0 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 271 users visited in the last hour